Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA-seq and flow cytometry to T cells, B cells, monocytes and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis. Utilizing an integrated strategy based on canonical correlation analysis of 5,265 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass cytometry and transcriptomics together revealed cell states expanded in RA synovia: THY1(CD90)(+)HLA-DRA(hi) sublining fibroblasts, IL1B(+) pro-inflammatory monocytes, ITGAX(+)TBX21(+) autoimmune-associated B cells and PDCD1(+) T peripheral helper (Tph) and T follicular helper (Tfh). We defined distinct subsets of CD8(+) T cells characterized by a GZMK(+), GZMB(+) and GNLY(+) phenotype. We mapped inflammatory mediators to their source cell populations; for example, we attributed IL6 expression to THY1(+)HLA-DRA(hi) fibroblasts, and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis.